setwd(“/Users/lotterhos/Library/CloudStorage/GoogleDrive-k.lotterhos@gmail.com/.shortcut-targets-by-id/1DPJy8RgFslz3_PSZLLl7Z21mCvQUvnJZ/Manuscripts/Cod Ecotypes GoM /data”)
#install_github(“jokergoo/ComplexHeatmap”) Didn’t install #didn’t install BiocManager::install(“inveRsion”)
library(devtools)
## Loading required package: usethis
library(bigstatsr)
library(bigsnpr)
library(ggplot2)
library(OutFLANK)
## Loading required package: qvalue
library(vegan)
## Loading required package: permute
##
## Attaching package: 'permute'
## The following object is masked from 'package:devtools':
##
## check
## Loading required package: lattice
## This is vegan 2.6-6.1
library(pheatmap)
bigSNP <- snp_attach(paste0("", "acod_merged.MAF05_QC.rds"))
# drop the individual at the 17th position because it is a duplicate. It was a fish that was right in the middle of being red or olive and it accidentally got left in both groups and got sequenced twice.
G_full <- bigSNP$genotypes[-17,]
pos_full <- bigSNP$map$physical.pos
samp_full <- bigSNP$fam$sample.ID[-17]
pop_full <- bigSNP$fam$family.ID[-17]
chrom_full <- bigSNP$map$chromosome
unique(chrom_full)
## [1] "NC_044048.1" "NC_044049.1" "NC_044050.1" "NC_044051.1" "NC_044052.1"
## [6] "NC_044053.1" "NC_044054.1" "NC_044055.1" "NC_044056.1" "NC_044057.1"
## [11] "NC_044058.1" "NC_044059.1" "NC_044060.1" "NC_044061.1" "NC_044062.1"
## [16] "NC_044063.1" "NC_044064.1" "NC_044065.1" "NC_044066.1" "NC_044067.1"
## [21] "NC_044068.1" "NC_044069.1" "NC_044070.1"
dim(G_full)
## [1] 294 2094293
NCORES <- nb_cores()
head(bigSNP$fam)
## family.ID sample.ID paternal.ID maternal.ID sex affection
## 1 Pop1 16216 0 0 0 -9
## 2 Pop1 16220 0 0 0 -9
## 3 Pop1 16224 0 0 0 -9
## 4 Pop1 16225 0 0 0 -9
## 5 Pop1 16229 0 0 0 -9
## 6 Pop1 16231 0 0 0 -9
head(samp_full)
## [1] 16216 16220 16224 16225 16229 16231
pop.names <- paste0("Pop", 1:9)
pop.IDs<- c("Mass.Winter",
"Mass.Red",
"Mass.Unknown",
"Cashes.Olive",
"Cashes.Red",
"Ice.SWOff",
"Ice.SWNear",
"Ice.NEOff",
"Ice.NENear")
region <- c(rep("GoM", 5), rep("Iceland", 4))
ecotype <- c(rep("Nearshore",5), "Migratory", "Nearshore",
"Migratory", "Nearshore")
pop.colors <- c(adjustcolor("darkgreen",1), #mass winter
adjustcolor("salmon",1), #mass red
adjustcolor("goldenrod3",0.5), #mass unknown
adjustcolor("darkgreen",0.75), #cashes olive
adjustcolor("salmon",0.75), #cashes red
adjustcolor("darkviolet",1), # Iceland SW Off
adjustcolor("cornflowerblue",0.5), #Iceland SW Near
adjustcolor("darkviolet",0.5), #Iceland NE Off
adjustcolor("cornflowerblue",1) #Iceland NE Near
)
write.table(data.frame(pop.names,pop.IDs, pop.colors, region, ecotype), "outputs/1-Pops.txt", row.names=FALSE)
samp_full <- data.frame(samp_full)
#Remove sample 17, duplicate
samp_full$Pop <- as.factor(bigSNP$fam$family.ID[-17])
# Add population name to smaple dataframe
samp_full$PopID <- factor(samp_full$Pop, ordered=TRUE)
levels(samp_full$PopID) = pop.IDs # this works because the
# populations are numbered
head(samp_full)
## samp_full Pop PopID
## 1 16216 Pop1 Mass.Winter
## 2 16220 Pop1 Mass.Winter
## 3 16224 Pop1 Mass.Winter
## 4 16225 Pop1 Mass.Winter
## 5 16229 Pop1 Mass.Winter
## 6 16231 Pop1 Mass.Winter
levels(samp_full$PopID)
## [1] "Mass.Winter" "Mass.Red" "Mass.Unknown" "Cashes.Olive" "Cashes.Red"
## [6] "Ice.SWOff" "Ice.SWNear" "Ice.NEOff" "Ice.NENear"
samp_full$Region <- "GoM"
samp_full$Region[samp_full$Pop %in% c("Pop6", "Pop7",
"Pop8", "Pop9")] = "Iceland"
samp_full$Ecotype <- "1-Nearshore"
samp_full$Ecotype[samp_full$Pop %in% c("Pop6", "Pop8")] <- "2-Migratory"
samp_full$Region <- as.factor(samp_full$Region)
samp_full$Ecotype <- as.factor(samp_full$Ecotype)
head(samp_full)
## samp_full Pop PopID Region Ecotype
## 1 16216 Pop1 Mass.Winter GoM 1-Nearshore
## 2 16220 Pop1 Mass.Winter GoM 1-Nearshore
## 3 16224 Pop1 Mass.Winter GoM 1-Nearshore
## 4 16225 Pop1 Mass.Winter GoM 1-Nearshore
## 5 16229 Pop1 Mass.Winter GoM 1-Nearshore
## 6 16231 Pop1 Mass.Winter GoM 1-Nearshore
tail(samp_full)
## samp_full Pop PopID Region Ecotype
## 289 18096 Pop9 Ice.NENear Iceland 1-Nearshore
## 290 18097 Pop9 Ice.NENear Iceland 1-Nearshore
## 291 18098 Pop9 Ice.NENear Iceland 1-Nearshore
## 292 18099 Pop9 Ice.NENear Iceland 1-Nearshore
## 293 18100 Pop9 Ice.NENear Iceland 1-Nearshore
## 294 18101 Pop9 Ice.NENear Iceland 1-Nearshore
samp_full$label <- paste(samp_full$Region,samp_full$Ecotype, samp_full$PopID, samp_full$samp_full, sep="_")
### colors for Region and Ecotype ####
samp_full$Region_color <- as.factor(samp_full$Region)
levels(samp_full$Region_color) <- c("blue4", "darkgoldenrod")
samp_full$Region_color <- as.character(samp_full$Region_color) # convert factor back to character
samp_full$Ecotype_color <- as.factor(samp_full$Ecotype)
levels(samp_full$Ecotype_color) <- c("darkcyan", "seagreen2")
samp_full$Ecotype_color <- as.character(samp_full$Ecotype_color) # convert factor back to character
### colors for populations ####
samp_full$PopID_color <- as.factor(samp_full$Pop)
levels(samp_full$PopID_color) <- pop.colors # this works because the populations are ordered by number
samp_full$PopID_color <- as.character(samp_full$PopID_color )
muts <- data.frame(chrom_full, pos_full, Glabel = paste(chrom_full,pos_full, sep="__"))
colnames(G_full) <- muts$Glabel
rownames(G_full) <- samp_full$label
set.seed(29435798)
index <- sort(sample(1:length(pos_full), 50000))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012)
# PCA
# make sure this is run on a code 256 type
# snp object, or it will run forever!
set.seed(6345082)
svd7 <- big_randomSVD(Gsub_snp,
snp_scaleBinom(),
ncores = NCORES,
k=2)
plot(svd7, type = "scores") +
aes(color = pop_full) +
labs(color = "Population")
pdf("figures/1-Gsub-PCA.pdf", width=5, height=5)
plot(svd7, type = "scores") +
aes(color = pop_full) +
labs(color = "Population")
dev.off()
## quartz_off_screen
## 2
# Add PC loadings to sample info
#samp_full$Gsub_PC1 <- svd7$u[,1]
#samp_full$Gsub_PC2 <- svd7$u[,2]
# Add PC loadings to muts
muts$Gsub_PC1 <- muts$Gsub_PC2 <-NA
muts$Gsub_PC1[index] <- svd7$v[,1]
muts$Gsub_PC2[index] <- svd7$v[,2]
plot(abs(muts$Gsub_PC1), pch=19, col=adjustcolor("blue",0.01))
index <- sort(which(muts$chrom_full=="NC_044048.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012)
set.seed(62385534)
svd7 <- big_randomSVD(Gsub_snp,
snp_scaleBinom(),
ncores = NCORES,
k=2)
muts$Gsub_LG1_PC1 <- NA
muts$Gsub_LG1_PC1[index] <- svd7$v[,1]
# Chrom 1
plot(muts$pos_full[muts$chrom_full=="NC_044048.1"],
abs(muts$Gsub_LG1_PC1[muts$chrom_full=="NC_044048.1"]),
pch=19, col=adjustcolor("blue",0.1),
main="LG1", ylab="PC1 loading", xlab="position (bp)")
(maxload1 <- quantile(abs(muts$Gsub_LG1_PC1), probs=0.99, na.rm=TRUE))
## 99%
## 0.006090969
abline(h=maxload1)
#start
LG1start <- min(which(abs(muts$Gsub_LG1_PC1)>maxload1))
LG1end <- max(which(abs(muts$Gsub_LG1_PC1)>maxload1))
muts[LG1start ,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 33090 NC_044048.1 11299038 NC_044048.1__11299038 NA NA 0.006117522
LG1start_minus1MB <- max(which(muts$pos_full<muts$pos_full[LG1start]-1000000 & muts$chrom_full=="NC_044048.1"))
muts[LG1start_minus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 29750 NC_044048.1 10298978 NC_044048.1__10298978 NA NA 0.0002175627
muts[LG1end,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 104012 NC_044048.1 28292263 NC_044048.1__28292263 NA NA
## Gsub_LG1_PC1
## 104012 0.006091121
LG1end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG1end]+1000000 & muts$chrom_full=="NC_044048.1"))
muts[LG1end_plus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 106154 NC_044048.1 29268531 NC_044048.1__29268531 NA NA
## Gsub_LG1_PC1
## 106154 -0.0005602807
plot(muts$pos_full[LG1start_minus1MB:LG1end_plus1MB],
abs(muts$Gsub_LG1_PC1[LG1start_minus1MB:LG1end_plus1MB]),
pch=19, col=adjustcolor("blue",0.1),
main="LG1", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG1start], col="orange", lwd=2)
abline(v=muts$pos_full[LG1end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")
index <- sort(which(muts$chrom_full=="NC_044049.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012)
set.seed(235540968)
svd7 <- big_randomSVD(Gsub_snp,
snp_scaleBinom(),
ncores = NCORES,
k=2)
muts$Gsub_LG2_PC1 <- NA
muts$Gsub_LG2_PC1[index] <- svd7$v[,1]
# Chrom 2
plot(muts$pos_full[muts$chrom_full=="NC_044049.1"],
abs(muts$Gsub_LG2_PC1[muts$chrom_full=="NC_044049.1"]),
pch=19, col=adjustcolor("blue",0.1),
main="LG2", ylab="PC1 loading", xlab="position (bp)")
(maxload1 <- quantile(abs(muts$Gsub_LG2_PC1), probs=0.99, na.rm=TRUE))
## 99%
## 0.01020831
abline(h=maxload1)
#start
LG2start <- min(which(abs(muts$Gsub_LG2_PC1)>maxload1))
LG2end <- max(which(abs(muts$Gsub_LG2_PC1)>maxload1))
muts[LG2start ,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 111433 NC_044049.1 481246 NC_044049.1__481246 NA NA NA
## Gsub_LG2_PC1
## 111433 0.01027682
LG2start_minus1MB <-min(which(muts$chrom_full=="NC_044049.1"))
# in this case it's just the start of the chromosome
muts[LG2start_minus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 109720 NC_044049.1 884 NC_044049.1__884 NA NA NA
## Gsub_LG2_PC1
## 109720 -0.0006092057
muts[LG2end,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 132871 NC_044049.1 4466546 NC_044049.1__4466546 NA NA NA
## Gsub_LG2_PC1
## 132871 0.01029919
LG2end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG2end]+1000000 & muts$chrom_full=="NC_044049.1"))
muts[LG2end_plus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 135332 NC_044049.1 5434591 NC_044049.1__5434591 NA NA NA
## Gsub_LG2_PC1
## 135332 0.0002754641
plot(muts$pos_full[LG2start_minus1MB:LG2end_plus1MB],
abs(muts$Gsub_LG2_PC1[LG2start_minus1MB:LG2end_plus1MB]),
pch=19, col=adjustcolor("blue",0.1),
main="LG2", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG2start], col="orange", lwd=2)
abline(v=muts$pos_full[LG2end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")
index <- sort(which(muts$chrom_full=="NC_044054.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012)
set.seed(42348064)
svd7 <- big_randomSVD(Gsub_snp,
snp_scaleBinom(),
ncores = NCORES,
k=2)
muts$Gsub_LG7_PC1 <- NA
muts$Gsub_LG7_PC1[index] <- svd7$v[,1]
# Chrom 7
plot(muts$pos_full[muts$chrom_full=="NC_044054.1"],
abs(muts$Gsub_LG7_PC1[muts$chrom_full=="NC_044054.1"]),
pch=19, col=adjustcolor("blue",0.1),
main="LG7", ylab="PC1 loading", xlab="position (bp)")
(maxload1 <- quantile(abs(muts$Gsub_LG7_PC1), probs=0.99, na.rm=TRUE))
## 99%
## 0.006244065
abline(h=maxload1)
#start
LG7start <- min(which(abs(muts$Gsub_LG7_PC1)>maxload1))
LG7end <- max(which(abs(muts$Gsub_LG7_PC1)>maxload1))
muts[LG7start ,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 648745 NC_044054.1 16828712 NC_044054.1__16828712 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 648745 NA NA -0.006261396
LG7start_minus1MB <-max(which(muts$pos_full<muts$pos_full[LG7start]-1000000 & muts$chrom_full=="NC_044054.1"))
# in this case it's just the start of the chromosome
muts[LG7start_minus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 645345 NC_044054.1 15828590 NC_044054.1__15828590 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 645345 NA NA 0.0002948823
muts[LG7end,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 696592 NC_044054.1 26336501 NC_044054.1__26336501 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 696592 NA NA -0.006245197
LG7end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG7end]+1000000 & muts$chrom_full=="NC_044054.1"))
muts[LG7end_plus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 700639 NC_044054.1 27336483 NC_044054.1__27336483 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 700639 NA NA -0.000523632
plot(muts$pos_full[LG7start_minus1MB:LG7end_plus1MB],
abs(muts$Gsub_LG7_PC1[LG7start_minus1MB:LG7end_plus1MB]),
pch=19, col=adjustcolor("blue",0.1),
main="LG7", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG7start], col="orange", lwd=2)
abline(v=muts$pos_full[LG7end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")
index <- sort(which(muts$chrom_full=="NC_044059.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012)
set.seed(73240982)
svd7 <- big_randomSVD(Gsub_snp,
snp_scaleBinom(),
ncores = NCORES,
k=2)
muts$Gsub_LG12_PC1 <- NA
muts$Gsub_LG12_PC1[index] <- svd7$v[,1]
# Chrom 12
plot(muts$pos_full[muts$chrom_full=="NC_044059.1"],
abs(muts$Gsub_LG12_PC1[muts$chrom_full=="NC_044059.1"]),
pch=19, col=adjustcolor("blue",0.1),
main="LG12", ylab="PC1 loading", xlab="position (bp)")
(maxload1 <- quantile(abs(muts$Gsub_LG12_PC1), probs=0.99, na.rm=TRUE))
## 99%
## 0.008958482
abline(h=maxload1)
#start
LG12start <- min(which(abs(muts$Gsub_LG12_PC1)>maxload1))
LG12end <- max(which(abs(muts$Gsub_LG12_PC1)>maxload1))
muts[LG12start ,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 1098771 NC_044059.1 1809214 NC_044059.1__1809214 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1098771 NA NA NA -0.008967974
LG12start_minus1MB <-max(which(muts$pos_full<muts$pos_full[LG12start]-1000000 & muts$chrom_full=="NC_044059.1"))
# in this case it's just the start of the chromosome
muts[LG12start_minus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 1096496 NC_044059.1 721009 NC_044059.1__721009 NA NA NA
## Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1096496 NA NA -0.004226609
muts[LG12end,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 1141346 NC_044059.1 13690550 NC_044059.1__13690550 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1141346 NA NA NA -0.009079696
LG12end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG12end]+1000000 & muts$chrom_full=="NC_044059.1"))
muts[LG12end_plus1MB,]
## chrom_full pos_full Glabel Gsub_PC2 Gsub_PC1
## 1142816 NC_044059.1 14677663 NC_044059.1__14677663 NA NA
## Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1142816 NA NA NA 2.969367e-05
plot(muts$pos_full[LG12start_minus1MB:LG12end_plus1MB],
abs(muts$Gsub_LG12_PC1[LG12start_minus1MB:LG12end_plus1MB]),
pch=19, col=adjustcolor("blue",0.1),
main="LG12", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG12start], col="orange", lwd=2)
abline(v=muts$pos_full[LG12end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")
breakpoints <- data.frame(
LG = c("LG1","LG2", "LG7","LG12"),
LGstartIndex = c(LG1start,LG2start,LG7start,LG12start),
LGendIndex = c(LG1end,LG2end,LG7end,LG12end),
chrom=chrom_full[c(LG1start,LG2start,LG7start,LG12start)],
LGstartPos = pos_full[c(LG1start,LG2start,LG7start,LG12start)],
LGendPos = pos_full[c(LG1end,LG2end,LG7end,LG12end)],
LGstartPos_minus1MB_index = c(LG1start_minus1MB,
LG2start_minus1MB,
LG7start_minus1MB,
LG12start_minus1MB),
LGendPos_plus1MB_index =c(LG1end_plus1MB,
LG2end_plus1MB,
LG7end_plus1MB,
LG12end_plus1MB)
)
LGind <- c(LG1start:LG1end, LG2start:LG2end,
LG7start:LG7end, LG12start:LG12end)
G_LG <- G_full[,LGind]
head(colnames(G_LG))
## [1] "NC_044048.1__11299038" "NC_044048.1__11299525" "NC_044048.1__11299592"
## [4] "NC_044048.1__11299650" "NC_044048.1__11302157" "NC_044048.1__11302179"
head(rownames(G_LG))
## [1] "GoM_1-Nearshore_Mass.Winter_16216" "GoM_1-Nearshore_Mass.Winter_16220"
## [3] "GoM_1-Nearshore_Mass.Winter_16224" "GoM_1-Nearshore_Mass.Winter_16225"
## [5] "GoM_1-Nearshore_Mass.Winter_16229" "GoM_1-Nearshore_Mass.Winter_16231"
dim(G_LG)
## [1] 294 182786
# Recode for bigsnpr package tools
G_LG_snp <- add_code256(big_copy(G_LG,type="raw"),code=bigsnpr:::CODE_012)
# PCA
# make sure this is run on a code 256 type
# snp object, or it will run forever!
set.seed(3459723)
svd7 <- big_randomSVD(G_LG_snp,
snp_scaleBinom(),
ncores = NCORES,
k=2)
samp_full$G_AllInv_PC1 <- svd7$u[,1]
samp_full$G_AllInv_PC2 <- svd7$u[,2]
pdf("figures/PCA-samples-inversion-SNPs-only.pdf", width=6, height=6)
ggplot(samp_full) + geom_point(aes(x=G_AllInv_PC1,
y=G_AllInv_PC2,
colour = PopID,
shape= Ecotype,
pch=Ecotype)) +
scale_colour_manual(values=pop.colors) +
xlab("Sample loadings PC1 - inversion SNPs only") +
ylab("Sample loadings PC2 - inversion SNPs only") +
theme_classic()
## Warning: Duplicated aesthetics after name standardisation: shape
## Duplicated aesthetics after name standardisation: shape
dev.off()
## quartz_off_screen
## 2
dist <- dist(G_LG, diag=TRUE)
str(dist)
## 'dist' num [1:43071] 297 281 298 287 256 ...
## - attr(*, "Size")= int 294
## - attr(*, "Labels")= chr [1:294] "GoM_1-Nearshore_Mass.Winter_16216" "GoM_1-Nearshore_Mass.Winter_16220" "GoM_1-Nearshore_Mass.Winter_16224" "GoM_1-Nearshore_Mass.Winter_16225" ...
## - attr(*, "Diag")= logi TRUE
## - attr(*, "Upper")= logi FALSE
## - attr(*, "method")= chr "euclidean"
## - attr(*, "call")= language dist(x = G_LG, diag = TRUE)
hc <- hclust(dist)
str(hc)
## List of 7
## $ merge : int [1:293, 1:2] -21 -8 -54 -223 -193 -218 -151 -138 7 -166 ...
## $ height : num [1:293] 104 110 119 196 198 ...
## $ order : int [1:294] 146 258 230 147 172 238 243 142 164 156 ...
## $ labels : chr [1:294] "GoM_1-Nearshore_Mass.Winter_16216" "GoM_1-Nearshore_Mass.Winter_16220" "GoM_1-Nearshore_Mass.Winter_16224" "GoM_1-Nearshore_Mass.Winter_16225" ...
## $ method : chr "complete"
## $ call : language hclust(d = dist)
## $ dist.method: chr "euclidean"
## - attr(*, "class")= chr "hclust"
dhc <- as.dendrogram(hc)
cut_avg <- cutree(hc, k = 5)
str(cut_avg)
## Named int [1:294] 1 1 2 1 1 1 1 1 1 1 ...
## - attr(*, "names")= chr [1:294] "GoM_1-Nearshore_Mass.Winter_16216" "GoM_1-Nearshore_Mass.Winter_16220" "GoM_1-Nearshore_Mass.Winter_16224" "GoM_1-Nearshore_Mass.Winter_16225" ...
str(dhc)
## --[dendrogram w/ 2 branches and 294 members at h = 554]
## |--[dendrogram w/ 2 branches and 97 members at h = 375]
## | |--[dendrogram w/ 2 branches and 54 members at h = 275]
## | | |--[dendrogram w/ 2 branches and 6 members at h = 219]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18014"
## | | | `--[dendrogram w/ 2 branches and 5 members at h = 215]
## | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18058"
## | | | `--[dendrogram w/ 2 branches and 4 members at h = 211]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18122"
## | | | `--[dendrogram w/ 2 branches and 3 members at h = 209]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18015"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 206]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18047"
## | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18131"
## | | `--[dendrogram w/ 2 branches and 48 members at h = 234]
## | | |--[dendrogram w/ 2 branches and 10 members at h = 214]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18138"
## | | | `--[dendrogram w/ 2 branches and 9 members at h = 213]
## | | | |--[dendrogram w/ 2 branches and 4 members at h = 210]
## | | | | |--[dendrogram w/ 2 branches and 2 members at h = 208]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18008"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.SWOff_18038"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 208]
## | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18029"
## | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18118"
## | | | `--[dendrogram w/ 2 branches and 5 members at h = 211]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18010"
## | | | `--[dendrogram w/ 2 branches and 4 members at h = 209]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18044"
## | | | `--[dendrogram w/ 2 branches and 3 members at h = 207]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18030"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 204]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18109"
## | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18124"
## | | `--[dendrogram w/ 2 branches and 38 members at h = 219]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18140"
## | | `--[dendrogram w/ 2 branches and 37 members at h = 217]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18147"
## | | `--[dendrogram w/ 2 branches and 36 members at h = 213]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18146"
## | | `--[dendrogram w/ 2 branches and 35 members at h = 212]
## | | |--[dendrogram w/ 2 branches and 32 members at h = 211]
## | | | |--[dendrogram w/ 2 branches and 30 members at h = 209]
## | | | | |--[dendrogram w/ 2 branches and 2 members at h = 207]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18001"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.SWOff_18049"
## | | | | `--[dendrogram w/ 2 branches and 28 members at h = 209]
## | | | | |--[dendrogram w/ 2 branches and 19 members at h = 207]
## | | | | | |--[dendrogram w/ 2 branches and 12 members at h = 206]
## | | | | | | |--[dendrogram w/ 2 branches and 8 members at h = 203]
## | | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18003"
## | | | | | | | `--[dendrogram w/ 2 branches and 7 members at h = 202]
## | | | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18141"
## | | | | | | | `--[dendrogram w/ 2 branches and 6 members at h = 201]
## | | | | | | | |--[dendrogram w/ 2 branches and 4 members at h = 199]
## | | | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18021"
## | | | | | | | | `--[dendrogram w/ 2 branches and 3 members at h = 198]
## | | | | | | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18170"
## | | | | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 196]
## | | | | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18113"
## | | | | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18128"
## | | | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 200]
## | | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18002"
## | | | | | | | `--leaf "Iceland_2-Migratory_Ice.SWOff_18046"
## | | | | | | `--[dendrogram w/ 2 branches and 4 members at h = 204]
## | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18013"
## | | | | | | `--[dendrogram w/ 2 branches and 3 members at h = 203]
## | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18031"
## | | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 199]
## | | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18106"
## | | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18133"
## | | | | | `--[dendrogram w/ 2 branches and 7 members at h = 206]
## | | | | | |--[dendrogram w/ 2 branches and 5 members at h = 204]
## | | | | | | |--[dendrogram w/ 2 branches and 2 members at h = 202]
## | | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18026"
## | | | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18130"
## | | | | | | `--[dendrogram w/ 2 branches and 3 members at h = 203]
## | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18025"
## | | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 201]
## | | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18040"
## | | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18125"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 205]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18034"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18149"
## | | | | `--[dendrogram w/ 2 branches and 9 members at h = 208]
## | | | | |--[dendrogram w/ 2 branches and 3 members at h = 206]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18103"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 203]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18104"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18112"
## | | | | `--[dendrogram w/ 2 branches and 6 members at h = 206]
## | | | | |--[dendrogram w/ 2 branches and 3 members at h = 205]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18126"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 203]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18108"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18151"
## | | | | `--[dendrogram w/ 2 branches and 3 members at h = 206]
## | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18143"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 204]
## | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18033"
## | | | | `--leaf "Iceland_2-Migratory_Ice.SWOff_18039"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 210]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18012"
## | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18150"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 211]
## | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18051"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 208]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18123"
## | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18139"
## | `--[dendrogram w/ 2 branches and 43 members at h = 344]
## | |--[dendrogram w/ 2 branches and 28 members at h = 299]
## | | |--[dendrogram w/ 2 branches and 4 members at h = 249]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18152"
## | | | `--[dendrogram w/ 2 branches and 3 members at h = 243]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18119"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 229]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18117"
## | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18148"
## | | `--[dendrogram w/ 2 branches and 24 members at h = 269]
## | | |--[dendrogram w/ 2 branches and 21 members at h = 236]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18127"
## | | | `--[dendrogram w/ 2 branches and 20 members at h = 232]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18142"
## | | | `--[dendrogram w/ 2 branches and 19 members at h = 229]
## | | | |--[dendrogram w/ 2 branches and 17 members at h = 226]
## | | | | |--[dendrogram w/ 2 branches and 3 members at h = 225]
## | | | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18075"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 223]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18017"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.SWOff_18032"
## | | | | `--[dendrogram w/ 2 branches and 14 members at h = 225]
## | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18037"
## | | | | `--[dendrogram w/ 2 branches and 13 members at h = 224]
## | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18019"
## | | | | `--[dendrogram w/ 2 branches and 12 members at h = 221]
## | | | | |--[dendrogram w/ 2 branches and 7 members at h = 220]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18048"
## | | | | | `--[dendrogram w/ 2 branches and 6 members at h = 219]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18024"
## | | | | | `--[dendrogram w/ 2 branches and 5 members at h = 217]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18132"
## | | | | | `--[dendrogram w/ 2 branches and 4 members at h = 216]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18006"
## | | | | | `--[dendrogram w/ 2 branches and 3 members at h = 214]
## | | | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18093"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 211]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18041"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18115"
## | | | | `--[dendrogram w/ 2 branches and 5 members at h = 221]
## | | | | |--[dendrogram w/ 2 branches and 3 members at h = 217]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18022"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 215]
## | | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18005"
## | | | | | `--leaf "Iceland_2-Migratory_Ice.SWOff_18043"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 218]
## | | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18020"
## | | | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18081"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 227]
## | | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18116"
## | | | `--leaf "Iceland_2-Migratory_Ice.NEOff_18120"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 242]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18186"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 228]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18136"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18083"
## | `--[dendrogram w/ 2 branches and 15 members at h = 313]
## | |--[dendrogram w/ 2 branches and 3 members at h = 246]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18187"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 226]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18160"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18078"
## | `--[dendrogram w/ 2 branches and 12 members at h = 247]
## | |--[dendrogram w/ 2 branches and 3 members at h = 223]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18052"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 218]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18059"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18091"
## | `--[dendrogram w/ 2 branches and 9 members at h = 233]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18099"
## | `--[dendrogram w/ 2 branches and 8 members at h = 232]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18082"
## | `--[dendrogram w/ 2 branches and 7 members at h = 230]
## | |--[dendrogram w/ 2 branches and 5 members at h = 225]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18110"
## | | `--[dendrogram w/ 2 branches and 4 members at h = 223]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18100"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 220]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18096"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 219]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18193"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18088"
## | `--[dendrogram w/ 2 branches and 2 members at h = 227]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18159"
## | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18162"
## `--[dendrogram w/ 2 branches and 197 members at h = 466]
## |--[dendrogram w/ 2 branches and 21 members at h = 363]
## | |--[dendrogram w/ 2 branches and 4 members at h = 307]
## | | |--[dendrogram w/ 2 branches and 2 members at h = 237]
## | | | |--leaf "GoM_1-Nearshore_Mass.Red_17016"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17283"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 252]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_17285"
## | | `--leaf "GoM_1-Nearshore_Mass.Red_17008"
## | `--[dendrogram w/ 2 branches and 17 members at h = 332]
## | |--[dendrogram w/ 2 branches and 3 members at h = 262]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18056"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 240]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18155"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18061"
## | `--[dendrogram w/ 2 branches and 14 members at h = 306]
## | |--[dendrogram w/ 2 branches and 5 members at h = 257]
## | | |--[dendrogram w/ 2 branches and 2 members at h = 229]
## | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18070"
## | | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18094"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 234]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18180"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 229]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18188"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18086"
## | `--[dendrogram w/ 2 branches and 9 members at h = 278]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_16241"
## | `--[dendrogram w/ 2 branches and 8 members at h = 252]
## | |--[dendrogram w/ 2 branches and 5 members at h = 232]
## | | |--[dendrogram w/ 2 branches and 3 members at h = 229]
## | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18084"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 228]
## | | | |--leaf "Iceland_2-Migratory_Ice.SWOff_18042"
## | | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18185"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 231]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18154"
## | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18175"
## | `--[dendrogram w/ 2 branches and 3 members at h = 233]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18179"
## | `--[dendrogram w/ 2 branches and 2 members at h = 230]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18161"
## | `--leaf "Iceland_1-Nearshore_Ice.NENear_18090"
## `--[dendrogram w/ 2 branches and 176 members at h = 401]
## |--[dendrogram w/ 2 branches and 99 members at h = 368]
## | |--[dendrogram w/ 2 branches and 10 members at h = 299]
## | | |--[dendrogram w/ 2 branches and 4 members at h = 250]
## | | | |--[dendrogram w/ 2 branches and 2 members at h = 228]
## | | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18189"
## | | | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18077"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 230]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18171"
## | | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18065"
## | | `--[dendrogram w/ 2 branches and 6 members at h = 270]
## | | |--[dendrogram w/ 2 branches and 3 members at h = 234]
## | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18062"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 225]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18173"
## | | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18190"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 241]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18164"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 219]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18194"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18092"
## | `--[dendrogram w/ 2 branches and 89 members at h = 358]
## | |--[dendrogram w/ 2 branches and 40 members at h = 302]
## | | |--[dendrogram w/ 2 branches and 22 members at h = 254]
## | | | |--[dendrogram w/ 2 branches and 8 members at h = 249]
## | | | | |--[dendrogram w/ 2 branches and 2 members at h = 246]
## | | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_17311"
## | | | | | `--leaf "GoM_1-Nearshore_Mass.Red_16211"
## | | | | `--[dendrogram w/ 2 branches and 6 members at h = 247]
## | | | | |--[dendrogram w/ 2 branches and 3 members at h = 244]
## | | | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_16227"
## | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 241]
## | | | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_16248"
## | | | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17240"
## | | | | `--[dendrogram w/ 2 branches and 3 members at h = 244]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Red_17273"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 239]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_17324"
## | | | | `--leaf "GoM_1-Nearshore_Mass.Unknown_17288"
## | | | `--[dendrogram w/ 2 branches and 14 members at h = 251]
## | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16220"
## | | | `--[dendrogram w/ 2 branches and 13 members at h = 249]
## | | | |--leaf "GoM_1-Nearshore_Mass.Red_17028"
## | | | `--[dendrogram w/ 2 branches and 12 members at h = 247]
## | | | |--[dendrogram w/ 2 branches and 3 members at h = 242]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16238"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 237]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_16240"
## | | | | `--leaf "GoM_1-Nearshore_Mass.Unknown_17292"
## | | | `--[dendrogram w/ 2 branches and 9 members at h = 244]
## | | | |--[dendrogram w/ 2 branches and 4 members at h = 239]
## | | | | |--[dendrogram w/ 2 branches and 2 members at h = 236]
## | | | | | |--leaf "GoM_1-Nearshore_Mass.Red_17010"
## | | | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17265"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 236]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17210"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17226"
## | | | `--[dendrogram w/ 2 branches and 5 members at h = 242]
## | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17248"
## | | | `--[dendrogram w/ 2 branches and 4 members at h = 239]
## | | | |--[dendrogram w/ 2 branches and 2 members at h = 235]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Red_17253"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17258"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 237]
## | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_17002"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17245"
## | | `--[dendrogram w/ 2 branches and 18 members at h = 259]
## | | |--[dendrogram w/ 2 branches and 7 members at h = 243]
## | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17206"
## | | | `--[dendrogram w/ 2 branches and 6 members at h = 239]
## | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_17033"
## | | | `--[dendrogram w/ 2 branches and 5 members at h = 236]
## | | | |--[dendrogram w/ 2 branches and 2 members at h = 232]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_17304"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17270"
## | | | `--[dendrogram w/ 2 branches and 3 members at h = 236]
## | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16231"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 231]
## | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16234"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17276"
## | | `--[dendrogram w/ 2 branches and 11 members at h = 248]
## | | |--[dendrogram w/ 2 branches and 2 members at h = 207]
## | | | |--leaf "GoM_1-Nearshore_Mass.Winter_17308"
## | | | `--leaf "GoM_1-Nearshore_Mass.Winter_17309"
## | | `--[dendrogram w/ 2 branches and 9 members at h = 245]
## | | |--[dendrogram w/ 2 branches and 6 members at h = 239]
## | | | |--[dendrogram w/ 2 branches and 2 members at h = 235]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16216"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17280"
## | | | `--[dendrogram w/ 2 branches and 4 members at h = 238]
## | | | |--[dendrogram w/ 2 branches and 2 members at h = 235]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Red_16219"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17211"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 236]
## | | | |--leaf "GoM_1-Nearshore_Mass.Red_17007"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17256"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 242]
## | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17242"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 234]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_16242"
## | | `--leaf "GoM_1-Nearshore_Mass.Winter_17306"
## | `--[dendrogram w/ 2 branches and 49 members at h = 339]
## | |--[dendrogram w/ 2 branches and 10 members at h = 294]
## | | |--[dendrogram w/ 2 branches and 5 members at h = 242]
## | | | |--[dendrogram w/ 2 branches and 3 members at h = 237]
## | | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18064"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 232]
## | | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18182"
## | | | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18097"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 241]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18183"
## | | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18184"
## | | `--[dendrogram w/ 2 branches and 5 members at h = 253]
## | | |--[dendrogram w/ 2 branches and 3 members at h = 231]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18165"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 228]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18166"
## | | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18174"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 239]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18172"
## | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18191"
## | `--[dendrogram w/ 2 branches and 39 members at h = 316]
## | |--[dendrogram w/ 2 branches and 7 members at h = 272]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_16229"
## | | `--[dendrogram w/ 2 branches and 6 members at h = 260]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_17286"
## | | `--[dendrogram w/ 2 branches and 5 members at h = 248]
## | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17224"
## | | `--[dendrogram w/ 2 branches and 4 members at h = 244]
## | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17260"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 238]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17155"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 235]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17314"
## | | `--leaf "GoM_1-Nearshore_Cashes.Red_17281"
## | `--[dendrogram w/ 2 branches and 32 members at h = 281]
## | |--[dendrogram w/ 2 branches and 22 members at h = 257]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_16232"
## | | `--[dendrogram w/ 2 branches and 21 members at h = 252]
## | | |--[dendrogram w/ 2 branches and 19 members at h = 250]
## | | | |--[dendrogram w/ 2 branches and 5 members at h = 247]
## | | | | |--[dendrogram w/ 2 branches and 2 members at h = 110]
## | | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16233"
## | | | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17233"
## | | | | `--[dendrogram w/ 2 branches and 3 members at h = 245]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Red_17262"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 239]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17221"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17252"
## | | | `--[dendrogram w/ 2 branches and 14 members at h = 249]
## | | | |--[dendrogram w/ 2 branches and 4 members at h = 246]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Red_17031"
## | | | | `--[dendrogram w/ 2 branches and 3 members at h = 245]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Red_17254"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 243]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Red_17024"
## | | | | `--leaf "GoM_1-Nearshore_Mass.Unknown_16228"
## | | | `--[dendrogram w/ 2 branches and 10 members at h = 247]
## | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16236"
## | | | `--[dendrogram w/ 2 branches and 9 members at h = 245]
## | | | |--[dendrogram w/ 2 branches and 3 members at h = 242]
## | | | | |--leaf "GoM_1-Nearshore_Cashes.Red_17268"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 239]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_17327"
## | | | | `--leaf "GoM_1-Nearshore_Mass.Red_17316"
## | | | `--[dendrogram w/ 2 branches and 6 members at h = 244]
## | | | |--leaf "GoM_1-Nearshore_Mass.Winter_16225"
## | | | `--[dendrogram w/ 2 branches and 5 members at h = 240]
## | | | |--[dendrogram w/ 2 branches and 3 members at h = 236]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Red_17027"
## | | | | `--[dendrogram w/ 2 branches and 2 members at h = 234]
## | | | | |--leaf "GoM_1-Nearshore_Mass.Winter_17294"
## | | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17272"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 237]
## | | | |--leaf "GoM_1-Nearshore_Mass.Red_17313"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Red_17279"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 251]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17026"
## | | `--leaf "GoM_1-Nearshore_Mass.Red_17153"
## | `--[dendrogram w/ 2 branches and 10 members at h = 263]
## | |--[dendrogram w/ 2 branches and 3 members at h = 247]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_16247"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 238]
## | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17230"
## | | `--leaf "GoM_1-Nearshore_Cashes.Red_17259"
## | `--[dendrogram w/ 2 branches and 7 members at h = 248]
## | |--[dendrogram w/ 2 branches and 3 members at h = 244]
## | | |--leaf "GoM_1-Nearshore_Cashes.Red_17271"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 241]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_17032"
## | | `--leaf "GoM_1-Nearshore_Mass.Red_17019"
## | `--[dendrogram w/ 2 branches and 4 members at h = 247]
## | |--leaf "GoM_1-Nearshore_Cashes.Red_17257"
## | `--[dendrogram w/ 2 branches and 3 members at h = 243]
## | |--leaf "GoM_1-Nearshore_Cashes.Olive_17204"
## | `--[dendrogram w/ 2 branches and 2 members at h = 236]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_16239"
## | `--leaf "GoM_1-Nearshore_Cashes.Red_17282"
## `--[dendrogram w/ 2 branches and 77 members at h = 384]
## |--[dendrogram w/ 2 branches and 30 members at h = 320]
## | |--[dendrogram w/ 2 branches and 12 members at h = 268]
## | | |--[dendrogram w/ 2 branches and 5 members at h = 249]
## | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17238"
## | | | `--[dendrogram w/ 2 branches and 4 members at h = 245]
## | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_17287"
## | | | `--[dendrogram w/ 2 branches and 3 members at h = 241]
## | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17234"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 236]
## | | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17236"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17249"
## | | `--[dendrogram w/ 2 branches and 7 members at h = 262]
## | | |--leaf "GoM_1-Nearshore_Cashes.Red_17261"
## | | `--[dendrogram w/ 2 branches and 6 members at h = 252]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17011"
## | | `--[dendrogram w/ 2 branches and 5 members at h = 242]
## | | |--leaf "GoM_1-Nearshore_Cashes.Olive_17219"
## | | `--[dendrogram w/ 2 branches and 4 members at h = 237]
## | | |--[dendrogram w/ 2 branches and 2 members at h = 232]
## | | | |--leaf "GoM_1-Nearshore_Mass.Unknown_16245"
## | | | `--leaf "GoM_1-Nearshore_Cashes.Olive_17215"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 235]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_17326"
## | | `--leaf "GoM_1-Nearshore_Mass.Unknown_17325"
## | `--[dendrogram w/ 2 branches and 18 members at h = 277]
## | |--[dendrogram w/ 2 branches and 11 members at h = 257]
## | | |--[dendrogram w/ 2 branches and 3 members at h = 232]
## | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18098"
## | | | `--[dendrogram w/ 2 branches and 2 members at h = 223]
## | | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18153"
## | | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18156"
## | | `--[dendrogram w/ 2 branches and 8 members at h = 243]
## | | |--leaf "Iceland_2-Migratory_Ice.NEOff_18134"
## | | `--[dendrogram w/ 2 branches and 7 members at h = 238]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18158"
## | | `--[dendrogram w/ 2 branches and 6 members at h = 236]
## | | |--[dendrogram w/ 2 branches and 2 members at h = 233]
## | | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18080"
## | | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18095"
## | | `--[dendrogram w/ 2 branches and 4 members at h = 233]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18067"
## | | `--[dendrogram w/ 2 branches and 3 members at h = 231]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18072"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 230]
## | | |--leaf "Iceland_1-Nearshore_Ice.NENear_18053"
## | | `--leaf "Iceland_1-Nearshore_Ice.NENear_18101"
## | `--[dendrogram w/ 2 branches and 7 members at h = 261]
## | |--[dendrogram w/ 2 branches and 2 members at h = 237]
## | | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18163"
## | | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18167"
## | `--[dendrogram w/ 2 branches and 5 members at h = 242]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18085"
## | `--[dendrogram w/ 2 branches and 4 members at h = 234]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18178"
## | `--[dendrogram w/ 2 branches and 3 members at h = 234]
## | |--leaf "Iceland_2-Migratory_Ice.SWOff_18035"
## | `--[dendrogram w/ 2 branches and 2 members at h = 231]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18069"
## | `--leaf "Iceland_1-Nearshore_Ice.NENear_18087"
## `--[dendrogram w/ 2 branches and 47 members at h = 356]
## |--[dendrogram w/ 2 branches and 3 members at h = 287]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18076"
## | `--[dendrogram w/ 2 branches and 2 members at h = 251]
## | |--leaf "GoM_1-Nearshore_Cashes.Olive_17203"
## | `--leaf "GoM_1-Nearshore_Cashes.Olive_17218"
## `--[dendrogram w/ 2 branches and 44 members at h = 333]
## |--[dendrogram w/ 2 branches and 6 members at h = 262]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18168"
## | `--[dendrogram w/ 2 branches and 5 members at h = 244]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18176"
## | `--[dendrogram w/ 2 branches and 4 members at h = 233]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18073"
## | `--[dendrogram w/ 2 branches and 3 members at h = 229]
## | |--leaf "Iceland_1-Nearshore_Ice.NENear_18074"
## | `--[dendrogram w/ 2 branches and 2 members at h = 224]
## | |--leaf "Iceland_1-Nearshore_Ice.SWNear_18157"
## | `--leaf "Iceland_1-Nearshore_Ice.SWNear_18192"
## `--[dendrogram w/ 2 branches and 38 members at h = 312]
## |--[dendrogram w/ 2 branches and 10 members at h = 259]
## | |--[dendrogram w/ 2 branches and 2 members at h = 240]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_16218"
## | | `--leaf "GoM_1-Nearshore_Cashes.Red_17278"
## | `--[dendrogram w/ 2 branches and 8 members at h = 248]
## | |--[dendrogram w/ 2 branches and 3 members at h = 243]
## | | |--leaf "GoM_1-Nearshore_Cashes.Red_17264"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 233]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17017"
## | | `--leaf "GoM_1-Nearshore_Mass.Red_17156"
## | `--[dendrogram w/ 2 branches and 5 members at h = 245]
## | |--[dendrogram w/ 2 branches and 2 members at h = 240]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17006"
## | | `--leaf "GoM_1-Nearshore_Mass.Red_17029"
## | `--[dendrogram w/ 2 branches and 3 members at h = 243]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_17296"
## | `--[dendrogram w/ 2 branches and 2 members at h = 104]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_17291"
## | `--leaf "GoM_1-Nearshore_Mass.Unknown_16221"
## `--[dendrogram w/ 2 branches and 28 members at h = 269]
## |--[dendrogram w/ 2 branches and 5 members at h = 243]
## | |--leaf "GoM_1-Nearshore_Mass.Red_17003"
## | `--[dendrogram w/ 2 branches and 4 members at h = 242]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_17298"
## | `--[dendrogram w/ 2 branches and 3 members at h = 239]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_16249"
## | `--[dendrogram w/ 2 branches and 2 members at h = 236]
## | |--leaf "GoM_1-Nearshore_Mass.Red_17001"
## | `--leaf "GoM_1-Nearshore_Cashes.Olive_17277"
## `--[dendrogram w/ 2 branches and 23 members at h = 257]
## |--leaf "GoM_1-Nearshore_Cashes.Olive_17216"
## `--[dendrogram w/ 2 branches and 22 members at h = 254]
## |--[dendrogram w/ 2 branches and 2 members at h = 119]
## | |--leaf "GoM_1-Nearshore_Mass.Red_17022"
## | `--leaf "GoM_1-Nearshore_Mass.Red_17023"
## `--[dendrogram w/ 2 branches and 20 members at h = 251]
## |--[dendrogram w/ 2 branches and 8 members at h = 244]
## | |--[dendrogram w/ 2 branches and 3 members at h = 241]
## | | |--leaf "GoM_1-Nearshore_Cashes.Red_17267"
## | | `--[dendrogram w/ 2 branches and 2 members at h = 240]
## | | |--leaf "GoM_1-Nearshore_Mass.Winter_17289"
## | | `--leaf "GoM_1-Nearshore_Cashes.Red_17263"
## | `--[dendrogram w/ 2 branches and 5 members at h = 244]
## | |--leaf "GoM_1-Nearshore_Mass.Winter_17303"
## | `--[dendrogram w/ 2 branches and 4 members at h = 241]
## | |--[dendrogram w/ 2 branches and 2 members at h = 234]
## | | |--leaf "GoM_1-Nearshore_Mass.Red_17020"
## | | `--leaf "GoM_1-Nearshore_Mass.Unknown_17290"
## | `--[dendrogram w/ 2 branches and 2 members at h = 235]
## | |--leaf "GoM_1-Nearshore_Mass.Red_16214"
## | `--leaf "GoM_1-Nearshore_Mass.Red_17013"
## `--[dendrogram w/ 2 branches and 12 members at h = 249]
## |--leaf "GoM_1-Nearshore_Mass.Red_17018"
## `--[dendrogram w/ 2 branches and 11 members at h = 246]
## |--leaf "GoM_1-Nearshore_Mass.Unknown_17030"
## `--[dendrogram w/ 2 branches and 10 members at h = 243]
## |--[dendrogram w/ 2 branches and 4 members at h = 239]
## | |--leaf "GoM_1-Nearshore_Mass.Unknown_16243"
## | `--[dendrogram w/ 2 branches and 3 members at h = 237]
## | |--leaf "GoM_1-Nearshore_Mass.Red_17154"
## | `--[dendrogram w/ 2 branches and 2 members at h = 232]
## | |--leaf "GoM_1-Nearshore_Mass.Unknown_16223"
## | `--leaf "GoM_1-Nearshore_Cashes.Olive_17235"
## `--[dendrogram w/ 2 branches and 6 members at h = 243]
## |--leaf "GoM_1-Nearshore_Mass.Winter_16224"
## `--[dendrogram w/ 2 branches and 5 members at h = 240]
## |--leaf "GoM_1-Nearshore_Mass.Red_17015"
## `--[dendrogram w/ 2 branches and 4 members at h = 238]
## |--leaf "GoM_1-Nearshore_Mass.Red_17315"
## `--[dendrogram w/ 2 branches and 3 members at h = 236]
## |--leaf "GoM_1-Nearshore_Mass.Red_17005"
## `--[dendrogram w/ 2 branches and 2 members at h = 233]
## |--leaf "GoM_1-Nearshore_Mass.Winter_17305"
## `--leaf "GoM_1-Nearshore_Mass.Winter_17317"
# https://www.datacamp.com/tutorial/hierarchical-clustering-R
pdf("figures/Hclust-inversionSNPsonly.pdf", width=15, height=10)
plot(hc, cex=0.3)
rect.hclust(hc , k = 5, border=2:6)
dev.off()
## quartz_off_screen
## 2
samp_full$InvHclustOrder <- hc$order
samp_full$InvHclustK5 <- as.numeric(cut_avg)
# this looks like SW near in Iceland is more closely related to GOM then NE NEar in Iceland
table(samp_full$PopID, samp_full$InvHclustK5)
##
## 1 2 3 4 5
## Mass.Winter 22 9 2 1 0
## Mass.Red 15 17 2 1 0
## Mass.Unknown 9 5 0 3 0
## Cashes.Olive 14 5 0 6 0
## Cashes.Red 19 4 1 1 0
## Ice.SWOff 0 0 1 1 37
## Ice.SWNear 14 4 8 6 8
## Ice.NEOff 0 0 0 1 38
## Ice.NENear 6 3 7 10 14
pdf("figures/Hclust-inversionSNPsonly-heatmap.pdf", width=15, height=15)
par(oma=c(8,4,4,8))
heatmap(as.matrix(dist), cexRow=0.2, cexCol=0.2, scale="none", ColSideColors=samp_full$PopID_color, RowSideColors=samp_full$PopID_color, )
dev.off()
## quartz_off_screen
## 2
head(samp_full)
## samp_full Pop PopID Region Ecotype
## 1 16216 Pop1 Mass.Winter GoM 1-Nearshore
## 2 16220 Pop1 Mass.Winter GoM 1-Nearshore
## 3 16224 Pop1 Mass.Winter GoM 1-Nearshore
## 4 16225 Pop1 Mass.Winter GoM 1-Nearshore
## 5 16229 Pop1 Mass.Winter GoM 1-Nearshore
## 6 16231 Pop1 Mass.Winter GoM 1-Nearshore
## label Region_color Ecotype_color PopID_color
## 1 GoM_1-Nearshore_Mass.Winter_16216 blue4 darkcyan #006400FF
## 2 GoM_1-Nearshore_Mass.Winter_16220 blue4 darkcyan #006400FF
## 3 GoM_1-Nearshore_Mass.Winter_16224 blue4 darkcyan #006400FF
## 4 GoM_1-Nearshore_Mass.Winter_16225 blue4 darkcyan #006400FF
## 5 GoM_1-Nearshore_Mass.Winter_16229 blue4 darkcyan #006400FF
## 6 GoM_1-Nearshore_Mass.Winter_16231 blue4 darkcyan #006400FF
## G_AllInv_PC1 G_AllInv_PC2 InvHclustOrder InvHclustK5
## 1 0.03531921 -0.007908553 146 1
## 2 0.06496404 -0.049032057 258 1
## 3 0.06134477 -0.053768027 230 2
## 4 0.05153129 -0.037532901 147 1
## 5 0.03185495 0.019557487 172 1
## 6 0.04147050 0.003228003 238 1
write.csv(samp_full,"outputs/1-Samples.csv")
saveRDS(samp_full,"outputs/1-Samples.rds")
breakpoints
## LG LGstartIndex LGendIndex chrom LGstartPos LGendPos
## 1 LG1 33090 104012 NC_044048.1 11299038 28292263
## 2 LG2 111433 132871 NC_044049.1 481246 4466546
## 3 LG7 648745 696592 NC_044054.1 16828712 26336501
## 4 LG12 1098771 1141346 NC_044059.1 1809214 13690550
## LGstartPos_minus1MB_index LGendPos_plus1MB_index
## 1 29750 106154
## 2 109720 135332
## 3 645345 700639
## 4 1096496 1142816
write.csv(breakpoints, "outputs/1-breakpoints.csv", row.names = FALSE)
head(G_full[,1:5]) # make sure rows and columns are labeled
## NC_044048.1__268 NC_044048.1__280
## GoM_1-Nearshore_Mass.Winter_16216 0 2
## GoM_1-Nearshore_Mass.Winter_16220 1 2
## GoM_1-Nearshore_Mass.Winter_16224 1 2
## GoM_1-Nearshore_Mass.Winter_16225 0 0
## GoM_1-Nearshore_Mass.Winter_16229 1 0
## GoM_1-Nearshore_Mass.Winter_16231 1 1
## NC_044048.1__378 NC_044048.1__539
## GoM_1-Nearshore_Mass.Winter_16216 0 1
## GoM_1-Nearshore_Mass.Winter_16220 0 0
## GoM_1-Nearshore_Mass.Winter_16224 0 0
## GoM_1-Nearshore_Mass.Winter_16225 0 0
## GoM_1-Nearshore_Mass.Winter_16229 0 0
## GoM_1-Nearshore_Mass.Winter_16231 0 0
## NC_044048.1__1555
## GoM_1-Nearshore_Mass.Winter_16216 0
## GoM_1-Nearshore_Mass.Winter_16220 0
## GoM_1-Nearshore_Mass.Winter_16224 0
## GoM_1-Nearshore_Mass.Winter_16225 0
## GoM_1-Nearshore_Mass.Winter_16229 0
## GoM_1-Nearshore_Mass.Winter_16231 0
saveRDS(G_LG, "outputs/1-AllLGSNPs.rds")
saveRDS(G_full[,LG1start_minus1MB:LG1end_plus1MB], "outputs/1-G_LG1.rds")
saveRDS(G_full[,LG2start_minus1MB:LG2end_plus1MB], "outputs/1-G_LG2.rds")
saveRDS(G_full[,LG7start_minus1MB:LG7end_plus1MB], "outputs/1-G_LG7.rds")
saveRDS(G_full[,LG12start_minus1MB:LG12end_plus1MB], "outputs/1-G_LG12.rds")